thanks for your help, it is difficult for me to imagine the effect of this
operation, but I have read a few places that this should be the effect, but
I might be wrong. Anyway, what I want is using two consecutive C-alphas as
"flexible hinges" rotating the peptide plane between this two C-alphas
around the imaginary bond between them leaving the coordinates of the rest
of the molecule unchanged. How would I accomplish this?
best, Jakob
2010/6/28 Robert Campbell <robert.campb...@queensu.ca>
> Dear Jakob,
>
> On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen <
> jtoudahl.niel...@gmail.com>
> wrote:
>
> > I would like to modify a protein pdb file with a "crankshaft" flip, which
> > is the anti-correlated double change: psi(i-1) += delta and phi(i) -=
> delta.
> > Such a change should leave the protein coordinates unchanged effecting
> only
> > atoms in residues i-1 and i. However implementation in pymol (see below)
> > changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
> > you help me? Can I somehow do the two changes simultanious?...
> >
> > set_dihedral 21/n, 21/ca, 21/c, 22/n, 148.435 #was 168.4
> > set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704 #was -103.7
>
> I don't see how this change can leave the other coordinates unchanged.
> Even
> if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the
> angles CA-C-N and C-N-CA are exactly the same, which they are not
> necessarily), rotation of the psi(i-1) bond will move the N(i) and
> CA(i) atoms, so therefore while a rotation in the opposite direction of the
> phi(i) bond will tend to keep the rest of the change travelling in the
> direction it was before those two counter-rotations, the backbone itself
> will
> be shifted. One textbook I consulted lists the angles at the C(i-1) and
> N(i)
> atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are
> not
> even theoretically going to be parallel. In practice, with "real"
> structures, they certainly are not usually going to be parallel.
>
> Cheers,
> Rob
>
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821 Fax: 613-533-2497
> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
>
>
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